input for ABSOLUTE for CCF calculation

[amootta]

Hi there, I've run FREEC on all of my tumour-normal matched samples to call somatic CNAs. I'm wondering if there is a way to make the input for ABSOLUTE, which requires the columns "Chromosome", "Start", "End", "Num_Probes" and "Segment_Mean". I would like to try and use it to calculate the CCF of my variants. Please let me know if possible

Thanks very much

[valeu]

Hi, no, currently FREEC does not output such a file. However, it can created based on the _ratio.txt output. Could you please share the first lines of the format you need?

[amootta]

Hi, thanks for your response. It would look something like this (this is just an example i pulled out of someone else's query elsewhere):

[valeu]

You can try this R script: FREEC_ratio2Absolute.zip You can run it as: cat FREEC_ratio2Absolute.R | R --slave --args <*_ratio.txt>

[valeu]

But keep in mind that you will get -inf if median ratio is 0. - Here FREEC outputs median and not mean. And the last column will be log2Median

[valeu]

I have also added it to https://github.com/BoevaLab/FREEC/tree/master/scripts